Soil microbiome research seeks to understand the diversity and abundance of microorganisms in various soil types as a function of environmental conditions. As a first step toward this goal, microbe nucleic acids must be extracted from the soil substrate. A major obstacle toward defining the soil microbiome is the ability to first culture these microorganisms to gain a better understanding of their ecology, diversity and species richness. Currently microbial cell culture media is selective and only certain isolates can be determined by this approach. As an alternative to the cell culture approach, a popular determination method is to directly extract and amplify microbial DNA from soil samples. Although this alternative method has given promising results, there remains hurdles that must be overcome. Most notably, soil is natively rich in substances such as humic acids, that inhibit polymerases and restriction enzymes making the amplification of DNA difficult. The bacterial communities within soil also present a significant hurdle when preparing samples for DNA extraction. The tough outer cell wall present in these bacteria, specifically, is the lynchpin for sample prep as time consuming enzymatic digestions remain a common method for bacterial lysis. High-energy, bead-based homogenization presents a time-saving solution for bacterial lysis from soil matrices prior to DNA extraction.
Herein, we evaluate the efficacy of the Omni Bead Ruptor Elite bead mill homogenizer in a soil DNA extraction workflow for downstream 16S rRNA detection via endpoint PCR.
Figure 1. Bacterial 16S rDNA Detection from soil. Lane 1: Molzym 1 kb Ladder, Lane 2-3: PCR product